The River Nile is considered the most important sources of fresh water for Egypt, supplying all agricultural, cultural needs (drinking water and other civilization uses), industry, and river navigation for transport and tourism ships and boat. Polynuclear aromatic hydrocarbons (PAHs) compounds are considered an important class of hazardous environmental contaminants because some exhibit carcinogenic or mutagenic properties. PAHs can be divided according to the number of rings into low and high molecular weights PAHs. The low molecular weights consist of two and three aromatic rings (LPAHs). While the high molecular weight consists of tetra-, penta and hexa- aromatic rings (HPAHs). Four to six ring PAHs is highly mutagenic and carcinogenic while two or three ring PAHs are less mutagenic but can be highly toxic. The concentrations of PAHs in the river water at the area of El-Qanater El-Khairiya and El-Waraq was determined in order to assess the anthropogenic chemical inputs from navigation activities of; touistic ships sailing and passenger transportation as well as to assess the weathering effect on the PAHs concentrations. Water samples were selected from ten sites from the main River Nile, Dameitta Branch, Rosetta Branch, El-Rahyaha El-Nassery, and El-Rahyaha El-Menofy in October 2010. Quantification of PAHs using high performance liquid chromatography technique was carried out. Concentration and spatial distribution of individual PAHs of the reference 16 PAHs listed by the United States Environmental Protection Agency (US-EPA) were investigated in surface water of the study area. The sources of 16 PAHs (pyogenic and perterogic) were achieved using both PAHs distribution and molecular indices based on ratios of selected PAHs concentrations. Total PAHs ranged from 620-1049 mu g/l with an average of 794 mu g/l. The highest value of total PAHs found in Dameitta Branch while the lowest one found in El-Rahyaha El-Nassery. The summation of LPAHs ranged from 1.3- 10.1 mu g/l, while the summation of HPAHs ranged from 615- 1047 mu g/l. The contamination in the study area was shown to be either pyrogenic or mixed pyrogenic and petrogenic. It was found that the PAHs in the study area were mainly derived from combustion coming from the traffics, heating system and run off. Meanwhile, the sources of pollution include petroleum-derived hydrocarbons which contributed to minor inputs. The obtained values can be considered to possess serious health hazards to both human health and all living organisms.